T-box Riboswitch Annotation Database - TBDB - TRAKTE from

T-box riboswitch TRAKTE

Putative TYR (GUA) T-box riboswitch from Pontibacillus chungwhensis BH030062

Source information

TBDB ID	TRAKTE
Host organism	Pontibacillus chungwhensis BH030062
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	AVBG01000015.1:24693-24430
Downstream protein description	tyrosine--tRNA ligase
Downstream protein ID	GenBank: KGP90167.1
T-box riboswitch length
Specifier loop sequence	UUACG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UAC
Predicted tRNA family	TYR (GUA)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence TRAKTE TAGTAAACCGAGAAGGGTTGAAGTAGTAAGTTGTTCCCTGTTTCAGAAAGCTGACGGTCGCTGTGAGTCAGTACAGAGCAAATTACGAATTACGTCCTGGAGTTTTCTTCTGATGATTTCAGAAGACGGGTGAATCCGTTATAAATTCCTTGAGTGGTAATCAGTTTGTCTGGTTACAACAAGGGTGGTACCGCGAGCGAGCCTCGTCCCTTTTTTAGGGGCGGGGTTTTTT

Predicted secondary structures

T-box riboswitch TRAKTE Antiterminator ......((......(((........((((.(.......(((........((((((...........))))))))).....).)))).........)))...))..(((((((.......)))))))(((......)))..................(((((((.......)))))))....((((.......(((((.....))))))))).....................

T-box riboswitch TRAKTE Terminator ......((......(((........((((.(.......(((........((((((...........))))))))).....).)))).........)))...))..(((((((.......)))))))(((......)))..................(((((((.......)))))))........................((((((((((.....))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UAC
Top predicted tRNA family: TYR (GUA)

Best tRNA match for top specifier >TYR (GUA) tRNA from Pontibacillus chungwhensis BH030062
GGAGGGGTAGCGAAGTTGGCCAAACGCGGCGGACTGTAAATCCGCTCCCTCTGGGTTCGCAGGTTCGAGTCCTGCCCCCTCCACCA

Predicted tRNA structure (((((((..(((............))).(((((.......))))).(((...)))...(((((.......))))))))))))....

Alternative specifier 1

Alternative 1 for predicted specifier: -
Alternative 1 for predicted tRNA family: -

Best tRNA match for alternative specifier 1 >TBDB tRNA pairing failed
tRNAscan-SE failed to find tRNA in host organism with anticodon matching predicted T-box specifier.

Predicted tRNA structure No tRNA structure predicted.

Alternative specifier 2

Alternative 2 for predicted specifier: -
Alternative 2 for predicted tRNA family: -

Best tRNA match for alternative specifier 2 >TBDB tRNA pairing failed
tRNAscan-SE failed to find tRNA in host organism with anticodon matching predicted T-box specifier.

Predicted tRNA structure No tRNA structure predicted.

Minimum Free Energy (MFE) Calculations

Folding MFE predictions

Antiterminator	ΔG° (kcal/mol)	-7.6
Terminator	ΔG° (kcal/mol	-18.3
	ΔΔG° (kcal/mol)

*Calculations performed using Vienna RNAeval at 37°C. More information available on methods avaialble on BioRXIV.

INFERNAL T-box riboswitch prediction output

Infernal prediction values

E-Value
Score	132.2
Bias	0.0
CM Accuracy	0.96

*More information about the meaning of these values can be found here.

T-box riboswitch structure prediction from input sequence

Feature	Length	Locus
Stem I		[7,103]
Stem II region
Stem III
Specifier region	-	[90,92]
T-box UGGN locus	-	[186,189]
Antiterminator		[182,211]
Terminator		[202,232]
All stems	-	[[7, 103], [106, 126], [127, 138], [157, 177], [182, 211]]

Input source sequence >AVBG01000015.1:24693-24430
TAGTAAACCGAGAAGGGTTGAAGTAGTAAGTTGTTCCCTGTTTCAGAAAGCTGACGGTCGCTGTGAGTCAGTACAGAGCAAATTACGAATTACGTCCTGGAGTTTTCTTCTGATGATTTCAGAAGACGGGTGAATCCGTTATAAATTCCTTGAGTGGTAATCAGTTTGTCTGGTTACAACAAGGGTGGTACCGCGAGCGAGCCTCGTCCCTTTTTTAGGGGCGGGGTTTTTT

INFERNAL output sequence >Infernal-AVBG01000015.1:24693-24430
UAGUAAACCGAGAAGGGUUGAAGUAGUAAGUUGUUCCCUGUUUCAGAAAGCUGACGGUCGCUGUGAGUCAGUACAGAGCAAAUUACGAAUUACGUCCUGGAGUUUUCUUCUGAUG------AUUUCAGAAGA-CGGGUGAAUCCGUUA-UAAAUUCCUUGAGUGGUAAUCA-GUUUGUCUGGUUACAACAAGGGUGGUACCGCGAGCGAGC-CUCGUCCCUUUU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AVBG01000015.1:24693-24430
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::